Metal complexes of cysteine have been studied using a density functional theory based method together with a continuum solvation model. Complexation geometries for metal complexes of cysteine with Zn2+, Mg2+, Ca2+, Fe3+, and Mn2+ have been determined. Different coordination modes have been considered for MCys(2) and MCys(3) complexes. Complexation energies have been determined, and they have been corrected with (empirical) metal- and ligand-specific parameters, the latter of which was determined separately for Cys(N,O,S) and Cys(N,S) ligands. The results indicate that the preferred binding mode for Zn2+ with cysteine is bidentate (N,S) type binding in tetrahedral or trigonal bipyramidal geometry while Mg2+ and Ca2+ prefer sulfur-free binding sites in octahedral geometry. Fe3+ prefers binding via sulfur and nitrogen atoms, whereas for Mn2+ several equally stable structures were found. The new correction parameters can be applied for other sulfur-containing ligands to evaluate the binding strength of a new ligand with metal ions. The observed preferences of metal ions in binding are in agreement with the previous knowledge of the behavior of metal ions.